On November 15, 2021, Science Advances announced the launch of The Human Proteoform Project. The ambitious project, led by the Consortium for Top-Down Proteomics, aims to address a critical next step in disease research. This means developing new technologies to outline a complete set of protein forms based on the ~20,000 genes in the human genome.Continue reading “An Ambitious Endeavor: The Human Proteoform Project”
A Quick Method for A Tailing PCR Products
Some thermostable DNA polymerases, including Taq, add a single nucleotide base extension to the 3′ end of amplified DNA fragments. These polymerases usually add an adenine, leaving an “A” overhang. There are several approaches to overcome the cloning difficulties presented by the presence of A overhangs on PCR products. One method involves treating the product with Klenow to create a blunt-ended fragment for subcloning. Another choice is to add restriction sites to the ends of your PCR fragments. You can do this by incorporating the desired restriction sites into the PCR primers. After amplification, the PCR product is digested and subcloned into the cloning vector. Take care when using this method, as not all restriction enzymes efficiently cleave at the ends of DNA fragments, and you may not be able to use every restriction enzyme you desire. There is some useful information about cutting with restriction sites close to the end of linear fragments in the Restriction Enzyme Resource Guide. Also, some restriction enzymes require extra bases outside the recognition site, adding further expense to the PCR primers as well as risk of priming to unrelated sequences in the genome.Continue reading “A Quick Method for A Tailing PCR Products”
Science Visitors Only: Watching Life Grow on a New Island
We spend a lot of time looking at history and imagining—”what was it like when…?” As a biologist, I find myself most drawn to stories about the evolution of life. Why does this plant have purplish leaves? How did this species end up in a symbiotic relationship with this other species? How did this animal get to this tiny island 20 miles off the Southern coast of Iceland?
That last one was too specific to be rhetorical, wasn’t it? The volcanic island of Surtsey broke the ocean surface on November 14, 1963, and continued to erupt until June 5, 1967, reaching its maximum size of 2.7 km2 (about the size of Central Park in New York City). At this size, it was large enough to be a good site for biocolonization. Only a few scientists are allowed to visit the island, ensuring that colonization of the island can occur without human interference. Continue reading “Science Visitors Only: Watching Life Grow on a New Island”
Extra extra: Read All About Tautonyms
If you’re active on #sciencetwitter, you may have seen a thread recently about tautonyms. “Tautonym” is a cool word for scientific names where the genus and species are the same word, For example, Vulpes vulpes is the scientific name for the red fox.
I have taken great delight in sharing these tautonyms with friends, colleagues, and random strangers on the bus. However, the problem that I keep having is that people want more details about something than the name. If you’ve had that problem, too, then this blog is for you. Continue reading “Extra extra: Read All About Tautonyms”
How Do You Defrost the Lab Freezer?
When I was in the lab, we usually started with an elaborate system of borrowed hairdryers and old chemistry ring stands. What is your preferred method of attacking a frost-full freezer?
Phylo: A Crowdsourced, Beautiful Biodiversity Game
They started with one provocative thought: “Kids know more about Pokemon than they do about the plants and animals in their backyard. We’d like to do something about that.”
And then the team behind the Science Creative Quarterly released the idea to the web to see what would happen. It was 2010.
Now, just a few years later, the resulting fruit of a crowdsourced labor is Phylo: The Trading Card Game. Phylo is a frankly beautiful, “sneakily educational”, immediately compelling and truly cross-functional collaboration of the artistic, gaming, scientific, education and even intellectual property law communities all coming together to create and curate a sort of “biodiversity Pokemon.”
Okay, sounds neat, but why?
Continue reading “Phylo: A Crowdsourced, Beautiful Biodiversity Game”
A Cup of Coffee, Hold the Rust
While at my desk early in the day last week, one headline struck me as particularly troubling: “Coffee Rust Regains Foothold”.
Reports from the Institute of Coffee of Costa Rica estimate that the latest coffee outbreak may cut by 50% the 2013-14 coffee harvest in that country. Coffee specialists in the U.S. are calling it the worst outbreak of rust in Mexico and Central America since rust arrived in the region, 40-some years ago.
And in Kenya, Africa, coffee rust has been described as causing ever-greater problems, even with Kenyan coffee varieties resistant to rust being grown.
Several Central American governments are enacting special legislation to fund projects against spread of the fungus.
It’s early February and in this little corner of the world, times seem tough. We are suddenly (although typically, for southern Wisconsin, USA) getting regular snowfalls: 3” this day, 6” a day later. It adds up to a lot of shoveling. There is nothing like a fresh snowfall and 30 minutes of shoveling to slow the morning commute. Continue reading “A Cup of Coffee, Hold the Rust”
How Is a Molecular Biologist Like a Computer Programmer?
My wife, the molecular biologist, tells me she spends her days “at the bench” and “in the hood.” There, she works with cells, plasmids, RNA, enzymes and buffers, incubators, water baths, columns, gels, filters and spectrophotometers. She transfers various quantities of liquids into and out of plastics and glassware. At least, that’s what I understand when I ask her, “how was your day?”
I can’t really understand her fascination with all of this, but then I don’t have to: I’m an app developer, a programmer who designs and builds applications for smartphones and tablets. My work day consists of sitting in front of a laptop, cranking out code. There’s the occasional break afforded by meetings and presentations, writing up design documents, sketching out how a user interface might look like. Then it’s back to the computer, and programming.
But in spite of these differences, there is a critical aspect of my wife’s work that, whenever she speaks of it, I immediately recognize in my own professional life: We both rely extensively on kits and components, and doing so profoundly affects the way that we approach our jobs. Continue reading “How Is a Molecular Biologist Like a Computer Programmer?”
How a Musical Petri Dish Could Waste Your Whole Morning
You know those things you occasionally come across that look kind of cool and you think might be good for a minute or two of diversion? You know how it’s all fine and dandy until you somehow get sucked in and, before you know it, half the day is gone? Yeah. Meet Seaquence.
Seaquence is an online web app created by Ryan Alexander, Gabriel Dunne, and Daniel Massey, with support from Gray Area Foundation for the Arts. It is described as “an experiment in musical composition,” where “adopting a biological metaphor, you can create and combine musical lifeforms resulting in an organic, dynamic composition.” It’s basically an online petri dish where you add little squiggly creatures that make music. You control what combination of sounds each creature makes by adding antennae or changing the wiggle pattern of their bodies. When you’re done, you have a little virtual ambient orchestra; an ecosystem of minuscule musicians that you have guided, shaped and molded to your exact specifications. Oh, the power! Muaaa-haa-haa! Continue reading “How a Musical Petri Dish Could Waste Your Whole Morning”
Inviting Mother Nature to the design table
Sustainability is all over the news these days. Green this, eco-friendly that, recycle everything, buy the twisty lightbulbs, and “Aren’t you going to compost that?” Much like good compost, sustainability is hot, and it’s finding its way not only into our households, but also into product design. Principles like using low-impact materials, energy efficiency and designing for reuse and renewability are increasing in importance. In ever-greater numbers, designers are looking to nature for inspiration as they create the next generation of innovative and sustainable products. It’s a burgeoning discipline called biomimicry. Continue reading “Inviting Mother Nature to the design table”